This function retrieves data for a specific group of primaryids, allowing for in-depth case-by-case evaluation and clinical reasoning. If MedDRA is available PTs are clustered by HLGT.
Usage
retrieve(
pids,
file_name = "individual_cases",
temp_reac = Reac,
temp_drug = Drug,
temp_demo = Demo,
temp_demo_supp = Demo_supp,
temp_outc = Outc,
temp_ther = Ther,
temp_doses = Doses,
temp_drug_supp = Drug_supp,
temp_indi = Indi,
temp_drug_name = Drug_name,
temp_meddra = NA,
temp_atc = NA,
save_in_excel = TRUE
)Arguments
- pids
Primaryids of interest.
- file_name
The name of the output xlsx file (default is "individual cases").
- temp_reac
Reac dataset. Can be set to sample_Reac for testing
- temp_drug
Drug dataset. Can be set to sample_Drug for testing
- temp_demo
Demo dataset. Defaults to Demo. Can be se to sample_Demo for testing
- temp_demo_supp
the Demo_supp databases. Can be set to sample_Demo_Supp for testing
- temp_outc
Outc dataset. Can be set to sample_Outc for testing
- temp_ther
Ther dataset. Can be set to sample_Ther for testing
- temp_doses
the Doses databases. Can be set to sample_Doses for testing
- temp_drug_supp
the Drug_supp databases. Can be set to sample_Drug_Supp for testing
- temp_indi
Indi dataset. Can be set to sample_Indi for testing
- temp_drug_name
the Drug_name databases. Can be set to sample_Drug_Name for testing
- temp_meddra
the MedDRA dictionary, if available. Defaults to NA for subscription requirement.
- temp_atc
the ATC classification, if available. Defaults to NA for testing.
- save_in_excel
Whether to save the outcome in an excel. Defaults to TRUE
Value
Two xlsx files with individual cases information: one general with a row per ICSR, and one with drug information and multiple rows per ICSR.
Examples
FAERS_version <- "24Q1"
pids <- sample_Demo[sex == "M"]$primaryid
if (file.exists("data/24Q1.csv")) {
retrieve(pids, save_in_excel = FALSE)
}